[BioC] Limit for chromosomal regions in biomaRt?

[Christian Ruckert]

I have a character vector of approximately 25000 genomic regions I want 
to retrieve additional genomic information for using biomaRt R-package:

library("biomaRt")
mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

regions = c(
"1:661517:668171",
"1:787463:794591"
...)

attribs = c("chromosome_name",
             "start_position",
             "end_position",
             "strand",
             "ensembl_gene_id",
             "hgnc_symbol")

result = getBM(filters="chromosomal_region", values=regions,
     attributes=attribs, mart=mart)

The above query seems to run forever (3 days +), but when splitting the 
regions vector in two halves each is finished after approximately 15 
minutes.

Am I doing something wrong or is there an upper limit for the number of 
regions in a biomart query?

Thanks in advance,
Christian


 > sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-pc-linux-gnu

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.4.0 IRanges_1.6.8 affy_1.26.1   Biobase_2.8.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-2           XML_3.1-0             affyio_1.16.0
[4] preprocessCore_1.10.0